Hey so I did the two quests as well as the puzzle, and yet still it show's as the dungeon not being cleared. When I hover over it on my map it says that I still need to explore it. I have gone in and out 4 times. I don't know what I'm missing....
I've not done this one, I rarely do group ones, but my first thought is that there's a room somewhere which only becomes available once you kill the boss in front of it.
I know I've been in there to grab the Skyshard, which is why I think there is a place I didn't get to which may be the case for you.
I did get to. I ran through it again even after talking to the guys wife and you know the quest complete thing showed up, it was only after for some reason when I logged on the next day, did it show that I cleared it. Weird but glad it resolved itself. I now have other issues.